GeneBe

rs57709964

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001080465.3(SPMAP1):​c.207+540_207+565delTTTTTTTTTTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000062 ( 0 hom., cov: 0)

Consequence

SPMAP1
NM_001080465.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.153

Publications

0 publications found
Variant links:
Genes affected
SPMAP1 (HGNC:34492): (sperm microtubule associated protein 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPMAP1NM_001080465.3 linkc.207+540_207+565delTTTTTTTTTTTTTTTTTTTTTTTTTT intron_variant Intron 1 of 2 ENST00000614158.2 NP_001073934.1 A8MV24

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPMAP1ENST00000614158.2 linkc.207+540_207+565delTTTTTTTTTTTTTTTTTTTTTTTTTT intron_variant Intron 1 of 2 2 NM_001080465.3 ENSP00000479396.1 A8MV24

Frequencies

GnomAD3 genomes
AF:
0.0000616
AC:
3
AN:
48696
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000896
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000694
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000616
AC:
3
AN:
48696
Hom.:
0
Cov.:
0
AF XY:
0.0000487
AC XY:
1
AN XY:
20518
show subpopulations
African (AFR)
AF:
0.0000896
AC:
1
AN:
11164
American (AMR)
AF:
0.00
AC:
0
AN:
2734
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
1626
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1818
South Asian (SAS)
AF:
0.00
AC:
0
AN:
888
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
568
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
56
European-Non Finnish (NFE)
AF:
0.0000694
AC:
2
AN:
28822
Other (OTH)
AF:
0.00
AC:
0
AN:
582
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.792
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs57709964; hg19: chr17-36996870; API